Just as we expect our members to not suggest someone has a mental disorder for merely believing LGBT issues are not a lifestyle choice (innate), it's also expected that we not suggest members have a mental disorder for believing it is a lifestyle choice (not innate).
The misuse (pejorative) use of the terms homophobic, transphobic, and the like should be flagged as rude. Suggesting someone that disagrees with your worldview has a serious mental condition is not constructive and is quite hypocritical, not to mention mostly inaccurate.
Let's all "Be Nice" and not assume malice, ignorance, or education level when discussing these issues with someone of the opposite viewpoint.
Premise for this question: For those not familiar with postfixes, a -phobia is: a combining form meaning “fear,” occurring in loanwords from Greek (hydrophobia); on this model, used in the names of mental disorders that have the general sense “dread of, aversion toward” that specified by the initial element. The core being: "...used in the names of mental disorders...that specified by the initial element." Plainly explained, any word of the form X-phobia, X being homo(sexual) in this case.
Analogy: We (SE) don't allow use of the medical term "retarded" as a descriptor (in all but extenuating circumstances), even though most people when misusing it meant "stupid." This widespread misuse of the term did not change its actual meaning. Replace homophobic with retarded in the cited thread and see how appalled this makes you.
Example: This question and some answers Throughout this question and answers, there are numerous usages of the term homophobic where it is used to describe someone that has the opposite viewpoint of the person, not apparently legitimate cases of a phobia. These are pejorative uses.
Sidenote: This meta question is essentially the same as this other one, but applied to a specific scenario. It's a bit strange the vote difference when it comes time to applying that principle.